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    <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="module.exports.html">exports</a></li></ul><h3>Global</h3><ul><li><a href="global.html#_bridgeDfs">_bridgeDfs</a></li><li><a href="global.html#_ccCountDfs">_ccCountDfs</a></li><li><a href="global.html#_ccGetDfs">_ccGetDfs</a></li><li><a href="global.html#_init">_init</a></li><li><a href="global.html#_initInfos">_initInfos</a></li><li><a href="global.html#add">add</a></li><li><a href="global.html#addAnchoredRing">addAnchoredRing</a></li><li><a href="global.html#addChild">addChild</a></li><li><a href="global.html#addEdge">addEdge</a></li><li><a href="global.html#addNeighbouringElement">addNeighbouringElement</a></li><li><a href="global.html#addRing">addRing</a></li><li><a href="global.html#addRingbondChild">addRingbondChild</a></li><li><a href="global.html#addRingConnection">addRingConnection</a></li><li><a href="global.html#addVertex">addVertex</a></li><li><a href="global.html#angle">angle</a></li><li><a href="global.html#annotateStereochemistry">annotateStereochemistry</a></li><li><a href="global.html#apothem">apothem</a></li><li><a href="global.html#areSetsEqual">areSetsEqual</a></li><li><a href="global.html#areVerticesInSameRing">areVerticesInSameRing</a></li><li><a href="global.html#atomicNumbers">atomicNumbers</a></li><li><a href="global.html#attachPseudoElement">attachPseudoElement</a></li><li><a href="global.html#averageDirection">averageDirection</a></li><li><a href="global.html#backupRingInformation">backupRingInformation</a></li><li><a href="global.html#backupRings">backupRings</a></li><li><a href="global.html#bonds">bonds</a></li><li><a href="global.html#bondsToAtoms">bondsToAtoms</a></li><li><a href="global.html#centralAngle">centralAngle</a></li><li><a href="global.html#chooseSide">chooseSide</a></li><li><a href="global.html#clear">clear</a></li><li><a href="global.html#clockwise">clockwise</a></li><li><a href="global.html#clone">clone</a></li><li><a href="global.html#contains">contains</a></li><li><a href="global.html#containsAll">containsAll</a></li><li><a href="global.html#containsRing">containsRing</a></li><li><a href="global.html#count">count</a></li><li><a href="global.html#createBridgedRing">createBridgedRing</a></li><li><a href="global.html#createNextBond">createNextBond</a></li><li><a href="global.html#createRing">createRing</a></li><li><a href="global.html#deepCopy">deepCopy</a></li><li><a href="global.html#degFactor">degFactor</a></li><li><a href="global.html#distance">distance</a></li><li><a href="global.html#distanceSq">distanceSq</a></li><li><a href="global.html#divide">divide</a></li><li><a href="global.html#divideScalar">divideScalar</a></li><li><a href="global.html#dot">dot</a></li><li><a href="global.html#draw">draw</a></li><li><a href="global.html#drawAromaticityRing">drawAromaticityRing</a></li><li><a href="global.html#drawBall">drawBall</a></li><li><a href="global.html#drawCircle">drawCircle</a></li><li><a href="global.html#drawDashedWedge">drawDashedWedge</a></li><li><a href="global.html#drawDebugPoint">drawDebugPoint</a></li><li><a href="global.html#drawDebugText">drawDebugText</a></li><li><a href="global.html#drawEdge">drawEdge</a></li><li><a href="global.html#drawEdges">drawEdges</a></li><li><a href="global.html#drawLine">drawLine</a></li><li><a href="global.html#drawPoint">drawPoint</a></li><li><a href="global.html#drawText">drawText</a></li><li><a href="global.html#drawVertices">drawVertices</a></li><li><a href="global.html#drawWedge">drawWedge</a></li><li><a href="global.html#each">each</a></li><li><a href="global.html#eachMember">eachMember</a></li><li><a href="global.html#edgeRingCount">edgeRingCount</a></li><li><a href="global.html#equals">equals</a></li><li><a href="global.html#extend">extend</a></li><li><a href="global.html#get">get</a></li><li><a href="global.html#getAdjacencyList">getAdjacencyList</a></li><li><a href="global.html#getAdjacencyMatrix">getAdjacencyMatrix</a></li><li><a href="global.html#getAngle">getAngle</a></li><li><a href="global.html#getAtomicNumber">getAtomicNumber</a></li><li><a href="global.html#getAttachedPseudoElements">getAttachedPseudoElements</a></li><li><a href="global.html#getAttachedPseudoElementsCount">getAttachedPseudoElementsCount</a></li><li><a href="global.html#getBondCount">getBondCount</a></li><li><a href="global.html#getBridgedRingRings">getBridgedRingRings</a></li><li><a href="global.html#getBridgedRings">getBridgedRings</a></li><li><a href="global.html#getBridges">getBridges</a></li><li><a href="global.html#getChargeText">getChargeText</a></li><li><a href="global.html#getClosestVertex">getClosestVertex</a></li><li><a href="global.html#getColor">getColor</a></li><li><a href="global.html#getCommonRingbondNeighbour">getCommonRingbondNeighbour</a></li><li><a href="global.html#getCommonRings">getCommonRings</a></li><li><a href="global.html#getComponentsAdjacencyMatrix">getComponentsAdjacencyMatrix</a></li><li><a href="global.html#getConnectedComponentCount">getConnectedComponentCount</a></li><li><a href="global.html#getConnectedComponents">getConnectedComponents</a></li><li><a href="global.html#getCurrentCenterOfMass">getCurrentCenterOfMass</a></li><li><a href="global.html#getCurrentCenterOfMassInNeigbourhood">getCurrentCenterOfMassInNeigbourhood</a></li><li><a href="global.html#getDistanceMatrix">getDistanceMatrix</a></li><li><a href="global.html#getDoubleBondCount">getDoubleBondCount</a></li><li><a href="global.html#getDrawnNeighbours">getDrawnNeighbours</a></li><li><a href="global.html#getEdge">getEdge</a></li><li><a href="global.html#getEdgeCount">getEdgeCount</a></li><li><a href="global.html#getEdgeList">getEdgeList</a></li><li><a href="global.html#getEdgeNormals">getEdgeNormals</a></li><li><a href="global.html#getEdges">getEdges</a></li><li><a href="global.html#getFusedRings">getFusedRings</a></li><li><a href="global.html#getHeavyAtomCount">getHeavyAtomCount</a></li><li><a href="global.html#getLargestOrAromaticCommonRing">getLargestOrAromaticCommonRing</a></li><li><a href="global.html#getLastVertexWithAngle">getLastVertexWithAngle</a></li><li><a href="global.html#getLeftChiral">getLeftChiral</a></li><li><a href="global.html#getLeftElement">getLeftElement</a></li><li><a href="global.html#getLeftVector">getLeftVector</a></li><li><a href="global.html#getLength">getLength</a></li><li><a href="global.html#getMaxBonds">getMaxBonds</a></li><li><a href="global.html#getNeighbourCount">getNeighbourCount</a></li><li><a href="global.html#getNeighbours">getNeighbours</a></li><li><a href="global.html#getNextInRing">getNextInRing</a></li><li><a href="global.html#getNonRingNeighbours">getNonRingNeighbours</a></li><li><a href="global.html#getOrderedNeighbours">getOrderedNeighbours</a></li><li><a href="global.html#getOverlapScore">getOverlapScore</a></li><li><a href="global.html#getPathIncludedDistanceMatrices">getPathIncludedDistanceMatrices</a></li><li><a href="global.html#getPolygon">getPolygon</a></li><li><a href="global.html#getRightChiral">getRightChiral</a></li><li><a href="global.html#getRightElement">getRightElement</a></li><li><a href="global.html#getRightVector">getRightVector</a></li><li><a href="global.html#getRing">getRing</a></li><li><a href="global.html#getRingbondCount">getRingbondCount</a></li><li><a href="global.html#getRingbondType">getRingbondType</a></li><li><a href="global.html#getRingCandidates">getRingCandidates</a></li><li><a href="global.html#getRingConnection">getRingConnection</a></li><li><a href="global.html#getRingConnections">getRingConnections</a></li><li><a href="global.html#getRingCount">getRingCount</a></li><li><a href="global.html#getRings">getRings</a></li><li><a href="global.html#getRotateAwayFromAngle">getRotateAwayFromAngle</a></li><li><a href="global.html#getRotateToAngle">getRotateToAngle</a></li><li><a href="global.html#getRotateTowardsAngle">getRotateTowardsAngle</a></li><li><a href="global.html#getSize">getSize</a></li><li><a href="global.html#getSpanningTreeNeighbours">getSpanningTreeNeighbours</a></li><li><a href="global.html#getSpiros">getSpiros</a></li><li><a href="global.html#getSSSR">getSSSR</a></li><li><a href="global.html#getSubgraphAdjacencyList">getSubgraphAdjacencyList</a></li><li><a href="global.html#getSubgraphAdjacencyMatrix">getSubgraphAdjacencyMatrix</a></li><li><a href="global.html#getSubgraphDistanceMatrix">getSubgraphDistanceMatrix</a></li><li><a href="global.html#getSubringCenter">getSubringCenter</a></li><li><a href="global.html#getSubtreeOverlapScore">getSubtreeOverlapScore</a></li><li><a href="global.html#getTextDirection">getTextDirection</a></li><li><a href="global.html#getTotalOverlapScore">getTotalOverlapScore</a></li><li><a href="global.html#getTreeDepth">getTreeDepth</a></li><li><a href="global.html#getVertexList">getVertexList</a></li><li><a href="global.html#getVertices">getVertices</a></li><li><a href="global.html#getVerticesAt">getVerticesAt</a></li><li><a href="global.html#hasBridgedRing">hasBridgedRing</a></li><li><a href="global.html#hasEdge">hasEdge</a></li><li><a href="global.html#haveCommonRingbond">haveCommonRingbond</a></li><li><a href="global.html#initPseudoElements">initPseudoElements</a></li><li><a href="global.html#initRings">initRings</a></li><li><a href="global.html#innerAngle">innerAngle</a></li><li><a href="global.html#intersection">intersection</a></li><li><a href="global.html#invert">invert</a></li><li><a href="global.html#isBenzeneLike">isBenzeneLike</a></li><li><a href="global.html#isBridge">isBridge</a></li><li><a href="global.html#isEdgeInRing">isEdgeInRing</a></li><li><a href="global.html#isEdgeRotatable">isEdgeRotatable</a></li><li><a href="global.html#isHeteroAtom">isHeteroAtom</a></li><li><a href="global.html#isInPolygon">isInPolygon</a></li><li><a href="global.html#isPartOfBridgedRing">isPartOfBridgedRing</a></li><li><a href="global.html#isPointInRing">isPointInRing</a></li><li><a href="global.html#isRingAromatic">isRingAromatic</a></li><li><a href="global.html#isSupersetOf">isSupersetOf</a></li><li><a href="global.html#isTerminal">isTerminal</a></li><li><a href="global.html#kkLayout">kkLayout</a></li><li><a href="global.html#length">length</a></li><li><a href="global.html#lengthSq">lengthSq</a></li><li><a href="global.html#mass">mass</a></li><li><a href="global.html#matrixToString">matrixToString</a></li><li><a href="global.html#maxBonds">maxBonds</a></li><li><a href="global.html#meanAngle">meanAngle</a></li><li><a href="global.html#merge">merge</a></li><li><a href="global.html#midpoint">midpoint</a></li><li><a href="global.html#multiply">multiply</a></li><li><a href="global.html#multiplyScalar">multiplyScalar</a></li><li><a href="global.html#neighbouringElementsEqual">neighbouringElementsEqual</a></li><li><a href="global.html#normalize">normalize</a></li><li><a href="global.html#normalized">normalized</a></li><li><a href="global.html#normals">normals</a></li><li><a href="global.html#parityOfPermutation">parityOfPermutation</a></li><li><a href="global.html#pathSetsContain">pathSetsContain</a></li><li><a href="global.html#polyCircumradius">polyCircumradius</a></li><li><a href="global.html#position">position</a></li><li><a href="global.html#print">print</a></li><li><a href="global.html#printRingInfo">printRingInfo</a></li><li><a href="global.html#radFactor">radFactor</a></li><li><a href="global.html#relativeClockwise">relativeClockwise</a></li><li><a href="global.html#remove">remove</a></li><li><a href="global.html#removeAll">removeAll</a></li><li><a href="global.html#removeRing">removeRing</a></li><li><a href="global.html#removeRingConnection">removeRingConnection</a></li><li><a href="global.html#removeRingConnectionsBetween">removeRingConnectionsBetween</a></li><li><a href="global.html#removeUnique">removeUnique</a></li><li><a href="global.html#reset">reset</a></li><li><a href="global.html#resolvePrimaryOverlaps">resolvePrimaryOverlaps</a></li><li><a href="global.html#resolveSecondaryOverlaps">resolveSecondaryOverlaps</a></li><li><a href="global.html#restoreRingInformation">restoreRingInformation</a></li><li><a href="global.html#restoreRings">restoreRings</a></li><li><a href="global.html#rotate">rotate</a></li><li><a href="global.html#rotateAround">rotateAround</a></li><li><a href="global.html#rotateAwayFrom">rotateAwayFrom</a></li><li><a href="global.html#rotateDrawing">rotateDrawing</a></li><li><a href="global.html#rotateSubtree">rotateSubtree</a></li><li><a href="global.html#rotateTo">rotateTo</a></li><li><a href="global.html#rotateToXAxis">rotateToXAxis</a></li><li><a href="global.html#round">round</a></li><li><a href="global.html#sameSideAs">sameSideAs</a></li><li><a href="global.html#scalarProjection">scalarProjection</a></li><li><a href="global.html#scale">scale</a></li><li><a href="global.html#setBondType">setBondType</a></li><li><a href="global.html#setLeftVector">setLeftVector</a></li><li><a href="global.html#setParentVertexId">setParentVertexId</a></li><li><a href="global.html#setPosition">setPosition</a></li><li><a href="global.html#setPositionFromVector">setPositionFromVector</a></li><li><a href="global.html#setRightVector">setRightVector</a></li><li><a href="global.html#setRingCenter">setRingCenter</a></li><li><a href="global.html#setTheme">setTheme</a></li><li><a href="global.html#shorten">shorten</a></li><li><a href="global.html#shortenFrom">shortenFrom</a></li><li><a href="global.html#shortenLeft">shortenLeft</a></li><li><a href="global.html#shortenRight">shortenRight</a></li><li><a href="global.html#shortenTo">shortenTo</a></li><li><a href="global.html#sortByAtomicNumberDesc">sortByAtomicNumberDesc</a></li><li><a href="global.html#subtract">subtract</a></li><li><a href="global.html#threePointangle">threePointangle</a></li><li><a href="global.html#toDeg">toDeg</a></li><li><a href="global.html#toggle">toggle</a></li><li><a href="global.html#toRad">toRad</a></li><li><a href="global.html#toString">toString</a></li><li><a href="global.html#traverseBF">traverseBF</a></li><li><a href="global.html#traverseTree">traverseTree</a></li><li><a href="global.html#twoPI">twoPI</a></li><li><a href="global.html#unique">unique</a></li><li><a href="global.html#units">units</a></li><li><a href="global.html#updateOther">updateOther</a></li><li><a href="global.html#updateSize">updateSize</a></li><li><a href="global.html#visitStereochemistry">visitStereochemistry</a></li><li><a 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<div id="main">
    
    <h1 class="page-title">exports</h1>
    

    




<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A class representing the molecular graph.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">(parseTree, isomeric<span class="signature-attributes">opt</span>)</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="Graph.js.html">Graph.js</a>, <a href="Graph.js.html#line18">line 18</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>



    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>vertices</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Vertex></span>


            
            </td>

            

            

            <td class="description last"><p>The vertices of the graph.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>edges</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Edge></span>


            
            </td>

            

            

            <td class="description last"><p>The edges of this graph.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>vertexIdsToEdgeId</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>A map mapping vertex ids to the edge between the two vertices. The key is defined as vertexAId + '_' + vertexBId.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>elementCount</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>A map associating element symbols with the number of occurences in this graph.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isometric</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not the SMILES associated with this graph is isometric.</p></td>
        </tr>

    
    </tbody>
</table>






<div class="description">
    <p>The constructor of the class Graph.</p>
</div>











    <h5>Parameters:</h5>
    

<table class="params">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        
        <th>Attributes</th>
        

        
        <th>Default</th>
        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>parseTree</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            
                <td class="attributes">
                

                

                
                </td>
            

            
                <td class="default">
                
                </td>
            

            <td class="description last"><p>A SMILES parse tree.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isomeric</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>false</code>
                
                </td>
            

            <td class="description last"><p>A boolean specifying whether or not the SMILES is isomeric.</p></td>
        </tr>

    
    </tbody>
</table>
















    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A static class containing helper functions for math-related tasks.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">()</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="MathHelper.js.html">MathHelper.js</a>, <a href="MathHelper.js.html#line4">line 4</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>





























    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A class representing a vertex.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">(value, x<span class="signature-attributes">opt</span>, y<span class="signature-attributes">opt</span>)</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line27">line 27</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>



    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>id</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The id of this vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>value</code></td>
            

            <td class="type">
            
                
<span class="param-type">Atom</span>


            
            </td>

            

            

            <td class="description last"><p>The atom associated with this vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>position</code></td>
            

            <td class="type">
            
                
<span class="param-type">Vector2</span>


            
            </td>

            

            

            <td class="description last"><p>The position of this vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>previousPosition</code></td>
            

            <td class="type">
            
                
<span class="param-type">Vector2</span>


            
            </td>

            

            

            <td class="description last"><p>The position of the previous vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>parentVertexId</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>
|

<span class="param-type">null</span>


            
            </td>

            

            

            <td class="description last"><p>The id of the previous vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>children</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>The ids of the children of this vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>spanningTreeChildren</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>The ids of the children of this vertex as defined in the spanning tree defined by the SMILES.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>edges</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>The ids of edges associated with this vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>positioned</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this vertex has been positioned.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>angle</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The angle of this vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>dir</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The direction of this vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>neighbourCount</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The number of neighbouring vertices.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>neighbours</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>The vertex ids of neighbouring vertices.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>neighbouringElements</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;String></span>


            
            </td>

            

            

            <td class="description last"><p>The element symbols associated with neighbouring vertices.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>forcePositioned</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this vertex was positioned using a force-based approach.</p></td>
        </tr>

    
    </tbody>
</table>






<div class="description">
    <p>The constructor for the class Vertex.</p>
</div>











    <h5>Parameters:</h5>
    

<table class="params">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        
        <th>Attributes</th>
        

        
        <th>Default</th>
        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>value</code></td>
            

            <td class="type">
            
                
<span class="param-type">Atom</span>


            
            </td>

            
                <td class="attributes">
                

                

                
                </td>
            

            
                <td class="default">
                
                </td>
            

            <td class="description last"><p>The value associated with this vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>x</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>0</code>
                
                </td>
            

            <td class="description last"><p>The initial x coordinate of the positional vector of this vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>y</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>0</code>
                
                </td>
            

            <td class="description last"><p>The initial y coordinate of the positional vector of this vertex.</p></td>
        </tr>

    
    </tbody>
</table>
















    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A class representing a ring connection.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">(firstRing, secondRing)</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="RingConnection.js.html">RingConnection.js</a>, <a href="RingConnection.js.html#line13">line 13</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>



    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>id</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The id of this ring connection.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>firstRingId</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>A ring id.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>secondRingId</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>A ring id.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>vertices</code></td>
            

            <td class="type">
            
                
<span class="param-type">Set.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>A set containing the vertex ids participating in the ring connection.</p></td>
        </tr>

    
    </tbody>
</table>






<div class="description">
    <p>The constructor for the class RingConnection.</p>
</div>











    <h5>Parameters:</h5>
    

<table class="params">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>firstRing</code></td>
            

            <td class="type">
            
                
<span class="param-type">Ring</span>


            
            </td>

            

            

            <td class="description last"><p>A ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>secondRing</code></td>
            

            <td class="type">
            
                
<span class="param-type">Ring</span>


            
            </td>

            

            

            <td class="description last"><p>A ring.</p></td>
        </tr>

    
    </tbody>
</table>
















    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A static class containing helper functions for array-related tasks.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">()</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="ArrayHelper.js.html">ArrayHelper.js</a>, <a href="ArrayHelper.js.html#line6">line 6</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>





























    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A class representing a ring.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">(members)</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="Ring.js.html">Ring.js</a>, <a href="Ring.js.html#line25">line 25</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>



    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>id</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The id of this ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>members</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>An array containing the vertex ids of the ring members.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>edges</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>An array containing the edge ids of the edges between the ring members.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>insiders</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>An array containing the vertex ids of the vertices contained within the ring if it is a bridged ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>neighbours</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>An array containing the ids of neighbouring rings.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>positioned</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this ring has been positioned.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>center</code></td>
            

            <td class="type">
            
                
<span class="param-type">Vector2</span>


            
            </td>

            

            

            <td class="description last"><p>The center of this ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>rings</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Ring></span>


            
            </td>

            

            

            <td class="description last"><p>The rings contained within this ring if this ring is bridged.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isBridged</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean whether or not this ring is bridged.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isPartOfBridged</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean whether or not this ring is part of a bridge ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isSpiro</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean whether or not this ring is part of a spiro.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isFused</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean whether or not this ring is part of a fused ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>centralAngle</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The central angle of this ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>canFlip</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this ring allows flipping of attached vertices to the inside of the ring.</p></td>
        </tr>

    
    </tbody>
</table>






<div class="description">
    <p>The constructor for the class Ring.</p>
</div>











    <h5>Parameters:</h5>
    

<table class="params">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>members</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>An array containing the vertex ids of the members of the ring to be created.</p></td>
        </tr>

    
    </tbody>
</table>
















    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>The main class of the application representing the smiles drawer</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">(options)</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="Drawer.js.html">Drawer.js</a>, <a href="Drawer.js.html#line27">line 27</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>



    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>graph</code></td>
            

            <td class="type">
            
                
<span class="param-type">Graph</span>


            
            </td>

            

            

            <td class="description last"><p>The graph associated with this SmilesDrawer.Drawer instance.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>ringIdCounter</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>An internal counter to keep track of ring ids.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>ringConnectionIdCounter</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>An internal counter to keep track of ring connection ids.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>canvasWrapper</code></td>
            

            <td class="type">
            
                
<span class="param-type">CanvasWrapper</span>


            
            </td>

            

            

            <td class="description last"><p>The CanvasWrapper associated with this SmilesDrawer.Drawer instance.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>totalOverlapScore</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The current internal total overlap score.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>defaultOptions</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>The default options.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>opts</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>The merged options.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>theme</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>The current theme.</p></td>
        </tr>

    
    </tbody>
</table>






<div class="description">
    <p>The constructor for the class SmilesDrawer.</p>
</div>











    <h5>Parameters:</h5>
    

<table class="params">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>options</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>An object containing custom values for different options. It is merged with the default options.</p></td>
        </tr>

    
    </tbody>
</table>
















    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A class representing an edge.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">(sourceId, targetId, weight<span class="signature-attributes">opt</span>)</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="Edge.js.html">Edge.js</a>, <a href="Edge.js.html#line15">line 15</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>



    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        
        <th>Attributes</th>
        

        
        <th>Default</th>
        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>id</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            
                <td class="attributes">
                

                
                </td>
            

            
                <td class="default">
                
                </td>
            

            <td class="description last"><p>The id of this edge.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>sourceId</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            
                <td class="attributes">
                

                
                </td>
            

            
                <td class="default">
                
                </td>
            

            <td class="description last"><p>The id of the source vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>targetId</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            
                <td class="attributes">
                

                
                </td>
            

            
                <td class="default">
                
                </td>
            

            <td class="description last"><p>The id of the target vertex.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>weight</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            
                <td class="attributes">
                

                
                </td>
            

            
                <td class="default">
                
                </td>
            

            <td class="description last"><p>The weight of this edge. That is, the degree of the bond (single bond = 1, double bond = 2, etc).</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>bondType</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                
                </td>
            

            
                <td class="default">
                
                    <code>'-'</code>
                
                </td>
            

            <td class="description last"><p>The bond type of this edge.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isPartOfAromaticRing</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                
                </td>
            

            
                <td class="default">
                
                    <code>false</code>
                
                </td>
            

            <td class="description last"><p>Whether or not this edge is part of an aromatic ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>center</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                
                </td>
            

            
                <td class="default">
                
                    <code>false</code>
                
                </td>
            

            <td class="description last"><p>Wheter or not the bond is centered. For example, this affects straight double bonds.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>wedge</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                
                </td>
            

            
                <td class="default">
                
                    <code>''</code>
                
                </td>
            

            <td class="description last"><p>Wedge direction. Either '', 'up' or 'down'</p></td>
        </tr>

    
    </tbody>
</table>






<div class="description">
    <p>The constructor for the class Edge.</p>
</div>











    <h5>Parameters:</h5>
    

<table class="params">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        
        <th>Attributes</th>
        

        
        <th>Default</th>
        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>sourceId</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            
                <td class="attributes">
                

                

                
                </td>
            

            
                <td class="default">
                
                </td>
            

            <td class="description last"><p>A vertex id.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>targetId</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            
                <td class="attributes">
                

                

                
                </td>
            

            
                <td class="default">
                
                </td>
            

            <td class="description last"><p>A vertex id.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>weight</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>1</code>
                
                </td>
            

            <td class="description last"><p>The weight of the edge.</p></td>
        </tr>

    
    </tbody>
</table>
















    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A class representing an atom.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">(element, bondType<span class="signature-attributes">opt</span>)</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="Atom.js.html">Atom.js</a>, <a href="Atom.js.html#line40">line 40</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>



    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>element</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            

            

            <td class="description last"><p>The element symbol of this atom. Single-letter symbols are always uppercase. Examples: H, C, F, Br, Si, ...</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>drawExplicit</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this atom is drawn explicitly (for example, a carbon atom). This overrides the default behaviour.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>ringbonds</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Object></span>


            
            </td>

            

            

            <td class="description last"><p>An array containing the ringbond ids and bond types as specified in the original SMILE.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>branchBond</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            

            

            <td class="description last"><p>The branch bond as defined in the SMILES.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>ringbonds[].id</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The ringbond id as defined in the SMILES.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>ringbonds[].bondType</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            

            

            <td class="description last"><p>The bond type of the ringbond as defined in the SMILES.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>rings</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>The ids of rings which contain this atom.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>bondType</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            

            

            <td class="description last"><p>The bond type associated with this array. Examples: -, =, #, ...</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isBridge</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this atom is part of a bridge in a bridged ring (contained by the largest ring).</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isBridgeNode</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this atom is a bridge node (a member of the largest ring in a bridged ring which is connected to a bridge-atom).</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>originalRings</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>Used to back up rings when they are replaced by a bridged ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>bridgedRing</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The id of the bridged ring if the atom is part of a bridged ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>anchoredRings</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Number></span>


            
            </td>

            

            

            <td class="description last"><p>The ids of the rings that are anchored to this atom. The centers of anchored rings are translated when this atom is translated.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>bracket</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>If this atom is defined as a bracket atom in the original SMILES, this object contains all the bracket information. Example: { hcount: {Number}, charge: ['--', '-', '+', '++'], isotope: {Number} }.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>plane</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>Specifies on which &quot;plane&quot; the atoms is in stereochemical deptictions (-1 back, 0 middle, 1 front).</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>attachedPseudoElements</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;Object></span>


            
            </td>

            

            

            <td class="description last"><p>A map with containing information for pseudo elements or concatinated elements. The key is comprised of the element symbol and the hydrogen count.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>attachedPseudoElement[].element</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            

            

            <td class="description last"><p>The element symbol.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>attachedPseudoElement[].count</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The number of occurences that match the key.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>attachedPseudoElement[].hyrogenCount</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The number of hydrogens attached to each atom matching the key.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>hasAttachedPseudoElements</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this attom will be drawn with an attached pseudo element or concatinated elements.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isDrawn</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this atom is drawn. In contrast to drawExplicit, the bond is drawn neither.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isConnectedToRing</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this atom is directly connected (but not a member of) a ring.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>neighbouringElements</code></td>
            

            <td class="type">
            
                
<span class="param-type">Array.&lt;String></span>


            
            </td>

            

            

            <td class="description last"><p>An array containing the element symbols of neighbouring atoms.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isPartOfAromaticRing</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this atom is part of an explicitly defined aromatic ring. Example: c1ccccc1.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>bondCount</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The number of bonds in which this atom is participating.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>chirality</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            

            

            <td class="description last"><p>The chirality of this atom if it is a stereocenter (R or S).</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>priority</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The priority of this atom acording to the CIP rules, where 0 is the highest priority.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>mainChain</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not this atom is part of the main chain (used for chirality).</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>hydrogenDirection</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            

            

            <td class="description last"><p>The direction of the hydrogen, either up or down. Only for stereocenters with and explicit hydrogen.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>subtreeDepth</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The depth of the subtree coming from a stereocenter.</p></td>
        </tr>

    
    </tbody>
</table>






<div class="description">
    <p>The constructor of the class Atom.</p>
</div>











    <h5>Parameters:</h5>
    

<table class="params">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        
        <th>Attributes</th>
        

        
        <th>Default</th>
        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>element</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            
                <td class="attributes">
                

                

                
                </td>
            

            
                <td class="default">
                
                </td>
            

            <td class="description last"><p>The one-letter code of the element.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>bondType</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>'-'</code>
                
                </td>
            

            <td class="description last"><p>The type of the bond associated with this atom.</p></td>
        </tr>

    
    </tbody>
</table>
















    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A class wrapping a canvas element.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">(target, theme, options)</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="CanvasWrapper.js.html">CanvasWrapper.js</a>, <a href="CanvasWrapper.js.html#line22">line 22</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>



    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>canvas</code></td>
            

            <td class="type">
            
                
<span class="param-type">HTMLElement</span>


            
            </td>

            

            

            <td class="description last"><p>The HTML element for the canvas associated with this CanvasWrapper instance.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>ctx</code></td>
            

            <td class="type">
            
                
<span class="param-type">CanvasRenderingContext2D</span>


            
            </td>

            

            

            <td class="description last"><p>The CanvasRenderingContext2D of the canvas associated with this CanvasWrapper instance.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>colors</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>The colors object as defined in the SmilesDrawer options.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>opts</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>The SmilesDrawer options.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>drawingWidth</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The width of the canvas.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>drawingHeight</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The height of the canvas.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>offsetX</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The horizontal offset required for centering the drawing.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>offsetY</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The vertical offset required for centering the drawing.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>fontLarge</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The large font size in pt.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>fontSmall</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The small font size in pt.</p></td>
        </tr>

    
    </tbody>
</table>






<div class="description">
    <p>The constructor for the class CanvasWrapper.</p>
</div>











    <h5>Parameters:</h5>
    

<table class="params">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>target</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>
|

<span class="param-type">HTMLElement</span>


            
            </td>

            

            

            <td class="description last"><p>The canvas id or the canvas HTMLElement.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>theme</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>A theme from the smiles drawer options.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>options</code></td>
            

            <td class="type">
            
                
<span class="param-type">Object</span>


            
            </td>

            

            

            <td class="description last"><p>The smiles drawer options object.</p></td>
        </tr>

    
    </tbody>
</table>
















    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A class representing a 2D vector.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">(x, y)</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="Vector2.js.html">Vector2.js</a>, <a href="Vector2.js.html#line9">line 9</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>



    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>x</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The x component of the vector.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>y</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The y component of the vector.</p></td>
        </tr>

    
    </tbody>
</table>






<div class="description">
    <p>The constructor of the class Vector2.</p>
</div>











    <h5>Parameters:</h5>
    

<table class="params">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>x</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>
|

<span class="param-type">Vector2</span>


            
            </td>

            

            

            <td class="description last"><p>The initial x coordinate value or, if the single argument, a Vector2 object.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>y</code></td>
            

            <td class="type">
            
                
<span class="param-type">Number</span>


            
            </td>

            

            

            <td class="description last"><p>The initial y coordinate value.</p></td>
        </tr>

    
    </tbody>
</table>
















    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A class encapsulating the functionality to find the smallest set of smallest rings in a graph.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">()</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="SSSR.js.html">SSSR.js</a>, <a href="SSSR.js.html#line5">line 5</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>





























    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>







<section>

<header>
    
        <h2>
        exports
        </h2>
        
            <div class="class-description"><p>A class representing a line.</p></div>
        
    
</header>

<article>
    <div class="container-overview">
    
        

    
    <h2>Constructor</h2>
    

    <h4 class="name" id="exports"><span class="type-signature"></span>new exports<span class="signature">(from<span class="signature-attributes">opt</span>, to<span class="signature-attributes">opt</span>, elementFrom<span class="signature-attributes">opt</span>, elementTo<span class="signature-attributes">opt</span>, chiralFrom<span class="signature-attributes">opt</span>, chiralTo<span class="signature-attributes">opt</span>)</span><span class="type-signature"></span></h4>

    




<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="Line.js.html">Line.js</a>, <a href="Line.js.html#line14">line 14</a>
    </li></ul></dd>
    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>



    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>from</code></td>
            

            <td class="type">
            
                
<span class="param-type">Vector2</span>


            
            </td>

            

            

            <td class="description last"><p>The Vector2 defining the start of the line.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>to</code></td>
            

            <td class="type">
            
                
<span class="param-type">Vector2</span>


            
            </td>

            

            

            <td class="description last"><p>The Vector2 defining the end of the line.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>elementFrom</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            

            

            <td class="description last"><p>The element symbol associated with the start of the line.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>elementTo</code></td>
            

            <td class="type">
            
                
<span class="param-type">String</span>


            
            </td>

            

            

            <td class="description last"><p>The element symbol associated with the end of the line.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>chiralFrom</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or not the source atom is a chiral center.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>chiralTo</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            

            

            <td class="description last"><p>A boolean indicating whether or tno the target atom is a chiral center.</p></td>
        </tr>

    
    </tbody>
</table>






<div class="description">
    <p>The constructor for the class Line.</p>
</div>











    <h5>Parameters:</h5>
    

<table class="params">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        
        <th>Attributes</th>
        

        
        <th>Default</th>
        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>from</code></td>
            

            <td class="type">
            
                
<span class="param-type">Vector2</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>new Vector2(0, 0)</code>
                
                </td>
            

            <td class="description last"><p>A vector marking the beginning of the line.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>to</code></td>
            

            <td class="type">
            
                
<span class="param-type">Vector2</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>new Vector2(0, 0)</code>
                
                </td>
            

            <td class="description last"><p>A vector marking the end of the line.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>elementFrom</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>null</code>
                
                </td>
            

            <td class="description last"><p>A one-letter representation of the element associated with the vector marking the beginning of the line.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>elementTo</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>null</code>
                
                </td>
            

            <td class="description last"><p>A one-letter representation of the element associated with the vector marking the end of the line.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>chiralFrom</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>false</code>
                
                </td>
            

            <td class="description last"><p>Whether or not the from atom is a chiral center.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>chiralTo</code></td>
            

            <td class="type">
            
                
<span class="param-type">Boolean</span>


            
            </td>

            
                <td class="attributes">
                
                    &lt;optional><br>
                

                

                
                </td>
            

            
                <td class="default">
                
                    <code>false</code>
                
                </td>
            

            <td class="description last"><p>Whether or not the to atom is a chiral center.</p></td>
        </tr>

    
    </tbody>
</table>
















    
    </div>

    

    

    

     

    

    

    

    

    
</article>

</section>




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